Differential expression of LncRNAs and mRNAs and their modulated network construction during the process of HIV transcription
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PROVIDER: PRJNA516813 | ENA |
REPOSITORIES: ENA
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Project description:Objective: Seek the differentially expressed mRNAs and long non-coding RNAs (LncRNAs) to construct the modulated network and seek for the hub LncRNAs during the process of human immunodeficiency virus (HIV) transcription. Method: Blood samples from HIV-infections were collected. They were divided into transcription active group and relatively inactive group based on the quantitative detection results of total HIV DNA and cell-association RNA (CA-RNA) from peripheral blood mononuclear cells (PBMCs). Individuals within each group were matched by age and genders. Microarray chips detection technology were utilized to detect and find the differentially expressed LncRNAs and mRNAs by statistical method of paired T test, then underwent some bioinformatics analysis. Result: 1240 differentially expressed genes (include 689 LncRNAs and 551 mRNAs) were found. Gene ontology analysis showed the differentially expressed mRNAs mainly enriched in positive or negative gene expression, immune cell formation or epigenetic regulation in the biological process; nucleosome, nucleolus, cytoplasm, nuclear chromatin in the cell component; RNA polymerase II regulatory region sequence-specific DNA binding, DNA, histone, and nucleic acid binding, transcription factor activity in molecular function. Pathway analysis showed the differentially expressed mRNAs enriched in the biological pathways such as systemic lupus erythematosus, alcoholism, cytokine-cytokine receptor interaction, RNA transport, mRNA surveillance pathway, Pathways in cancer, etc. Cis and trans analysis to the differentially expressed LncRNAs searching its targeted genes and then made intersection for the differentially expressed mRNAs, then constructed the modulated network between LncRNAs and mRNAs. Based on this modulated network, four hub transcripts were excavated and validated by quantitative real-time PCR to confirm the veracity of microarray analysis findings. Two hub transcripts of lnc-CCNYL1-1:2 and ZNF793 were found directly interacted in the modulated network and their level of expression transformed parallelly. Conclusion: Quantitative detection results of cellular levels of total HIV DNA and RNA can distinguish whether HIV is in the state of active transcription. During process of HIV transcription, the differentially expressed LncRNAs involve the biological process of gene expression regulation, the hub genes excavated form the modulated network may become the potential candidate targets for HIV antiviral treatment.
2022-01-24 | GSE125556 | GEO
Project description:Chemoresistance is a major cause of poor prognosis of breast cancer.More and more mRNAs and lncRNAs are reported to upregulate chemoresistance in breast cancer.To explore the how mRNAs and lncRNAs involved in chemoresistance of breast cancer,we sceened upregulated mRNAs and lncRNA from parental MCF-7 , chemoresistant MCF-7 cells as well as 4 breast cancer tissue sensitive to chemotherapy and 4 resistant to chemotherapy . Total RNA was extracted using Trizol reagent. Agilent Human lncRNA Microarray V6 (4*180K) was used to analyze the global profiling of human lncRNAs and protein-coding transcripts in these samples. The microarray contains 83,835 lncRNAs and 27,233 coding genes.
2020-02-25 | E-MTAB-8787 | biostudies-arrayexpress
Project description:Studying the effects of HIV infection on the host transcriptome has typically focused on protein-coding genes. However, recent advances in the field of RNA sequencing revealed that long non-coding RNAs (lncRNAs) add an extensive additional layer to the cell’s molecular network and are highly involved in the regulation of molecular processes, including gene expression. Here, we performed transcriptome profiling throughout a primary HIV infection in vitro to investigate lncRNA expression at the different HIV replication cycle processes (reverse transcription, integration and particle production). Subsequently, guilt-by-association, transcription factor and co-expression analysis were performed to infer biological roles for the lncRNAs identified in the HIV-host interplay. Many lncRNAs were shown to play a role in mechanisms relying on proteasomal and ubiquitinylation pathways, apoptosis, DNA damage responses and cell cycle regulation. Through transcription factor binding analysis, we found that lncRNAs display a distinct transcriptional regulation profile as compared to protein coding mRNAs, suggesting that mRNAs and lncRNAs are independently modulated from each other. In addition, we identified five differentially expressed lncRNA-mRNA pairs with mRNA involvement in HIV pathogenesis (HIV linked co-expression) with possible cis regulatory lncRNAs that control the nearby mRNA expression and function. Altogether, the present study demonstrates that lncRNAs add a new dimension to the HIV-host interplay and should be further investigated as they may represent targets for controlling HIV replication.
2016-10-31 | GSE74818 | GEO
Project description:Identification of LncRNAs and mRNAs involved in adipogenesis
| PRJNA788280 | ENA
Project description:Purporse: FPV can cause a viral disease that occurs in cats, causing severe leukopenia, gastro-enteritis and nervous signs and leads to significant losses. LncRNAs biochemically resemble mRNAs posited by Jacob and Monod, yet do not template protein synthesis. Rather, lncRNAs functioning as RNA genes to play an important role in many biological and pathological processes such as inflammation and viral infection. However, lncRNAs have not been comprehensively identified in felines. Here, microarrays of mRNAs and lncRNAs were globally performed to identify the lncRNAs related to immune response of feline panleukopenia virus infection in F81 cells. Methods:lncRNA and mRNA sequencing analysis was performed on an Illumina Hiseq 4000 (LC Sciences, USA) following the vendor's recommended protocol Results: Through RNA sequencing, we performed a comprehensive analysis of lncRNAs and mRNAs in FPV infected F81 cells. F81 cells infected or uninfected FPV were used to prepare six libraries to generate 14.66 to 15.45 gigabytes (GB) clean reads per sample. We obtained 90588 novel lncRNAs, and 291 are differential expressed lncRNAs between FPV infected cells and uninfected cells. Consistent with previous studies, lncRNAs showed features distinct from mRNAs, such as shorter lengths, lesser exon numbers, and lower expression levels compared to mRNAs. The GO enrichment and KEGG pathway analyses showed that a majority of genes and lncRNAs were mainly related to the immune response of host cells with FPV infection. By differentially expressed target genes as well as co-expression network construction analysis, 21 key differentially expressed genes (19 upregulated & 2 downregulated) related to immune regulation of FPV infection in F81 cells were identified. Moreover, fifteen differentially expressed genes (five lncRNAs, ten mRNAs) were selected and independently validated by reverse-transcription qPCR and the results were consistent with the sequencing results. Conclusion: The present study is the first to provide insights into the biological connection of lncRNAs and FPV infection, which can be further explore for the potential link between lncRNA expression and the pathogenesis of FPV infection.
2020-12-20 | GSE137896 | GEO
Project description:Sustained hepatic inflammation can contribute to cancer initiation and progression via tumor-initiating cell expansion, but underlying mechanisms remains unknown. Expression profiles of lncRNAs/mRNAs were measured in normal, chronic hepatitis, cirrhotic and cancerous livers. We found abundant disease-related lncRNAs/mRNAs deregulated across different stages of inflammation-triggered liver disease and refined a transformation gene signature to distinguish pathological liver tissues. Amongst this signature, a conserved lncRNA DANCR was silenced in normal adult liver, but overexpressed in fetal and cancerous livers. Remarkably, increased DANCR significantly correlates with poor prognosis in multiple-center cohorts and is directly induced by inflammatory pathways including NF-κB and STAT3. DANCR could suppress cell differentiation and drive expansion of tumor-initiating cells, leading to chemoresistance. Moreover, in vitro and in vivo inhibition confirms the significance of DANCR as a therapeutic target when combined with other chemotherapy. We illustrate the role of DANCR relies on the regulation of CTNNB1 in a novel miRNA-blocking manner. Our studies reveal the expression of lncRNAs/mRNAs in normal and pathological livers and suggest the importance of oncofetal lncRNA DANCR in inflammation-induced malignant transformation, offering a potential prognostic marker and a therapeutic target for HCC. In the study, 10 normal livers (NL), 10 chronic inflammatory livers (IL), 10 cirrhotic livers (CL), 13 early HCC (eHCC) and 13 advanced HCC (aHCC) samples were profiled their lncRNA/mRNA expression
2014-01-22 | E-GEOD-54238 | biostudies-arrayexpress
Project description:Autologous chondrocyte implantation (ACI) is an effective method to treat chronic articular cartilage injury in recent years, which requires a large number of human hyaline chondrocytes. Unfortunately, human hyaline chondrocytes often undergo dedifferentiation in vitro. Thus, it is important to elucidate the mechanism of dedifferentiation for the application of ACI technology. Long noncoding RNAs (lncRNA) play a regulatory role in gene expression in many pathological and physiological processes. However, the role of lncRNAs in human hyaline chondrocyte dedifferentiation remains unclear. The aim of this study was to investigate the expression profiles of lncRNAs in human hyaline chondrocyte dedifferentiation during in vitro culture. First, we cultured human hyaline chondrocytes in vitro and detected the expression of COL1A1, COL2A1, and SOX-9 in passage 1 (P1) and 5 (P5) chondrocytes using quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence, and western blotting. Then, we analyzed the expression profiles of lncRNAs and mRNAs in P1 and P5 chondrocytes by microarray analysis.
2020-02-25 | GSE145817 | GEO
Project description:Ossification of the ligamentum flava (OLF) is a common spinal disorder among the elderly that causes myelopathy and radiculopathy. Although studies have identified several genes that correlated with OLF, the underlying regulation network is far from clear. To identify transcriptional regulators for OLF, we compared the lncRNAs and mRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis, which revealed a panel of lncRNAs and mRNAs that were specifically regulated in ligament tissues of human undergoing ossification. To identify transcriptional regulators for OLF, we compared the lncRNAs and mRNAs expression of the ligamentum flava tissues from OLF patients and healthy volunteers through microarray analysis.
2017-10-27 | GSE106253 | GEO
Project description:Oral carcinogenesis is a multi-step process involving normal mucosa progressing to oral precancerous lesions and finally to oral squamous cell carcinoma (OSCC). This complex process encompasses various molecules, including non-coding RNAs (ncRNAs). In this study, we performed whole-transcriptome analyses on adjacent normal tissues, oral leukoplakia tissues, and OSCC tissues, with the goal of identifying key differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs associated with different stages of oral carcinogenesis. In our study, numerous differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs were identified in adjacent normal, oral leukoplakia, and OSCC tissues. Subsequently, we constructed two regulatory competitive endogenous RNA (ceRNA) networks and identified some potential critical molecules involved in oral carcinogenesis. In conclusion, based on the whole-transcriptome analyses, we mapped the molecular feathers at RNA level during the process of oral carcinogenesis and revealed certain ncRNAs with great research potential.
2023-10-26 | GSE246050 | GEO
Project description:Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), which were proved to play a crucial role in regulating cell differentiation and tissue development. However, the expression profiles of different RNAs, such as mRNA, lncRNAs, and circRNAs in different adipose tissues, are still largely unclear. To shed light on this issue, we performed the systematic analysis of mRNAs, lncRNAs, and circRNAs obtained from intramuscular adipose tissues (IAT), subcutaneous adipose tissues (SAT), visceral adipose tissues (RPAT), and mesenteric adipose tissues (MAT) tissues of Chinese Erhualian pigs using high-throughput sequencing. A total of 1,695, 1,878, 494, 1,300, 902, and 355 differentially expressed (DE) mRNAs, 318, 399, 192, 251, 249, and 347 DE lncRNAs, 1,367, 1,007, 999, 1,153, 1,256, and 837 DE circRNAs were identified in IAT versus SAT, IAT versus RPAT, SAT versus RPAT, MAT versus IAT, MAT versus SAT, and MAT versus RPAT, respectively. Gene ontology (GO) enrichment analyses showed these DE genes were mainly involved in lipid metabolic and immune response. Next the co-expression network construction of mRNAs-lncRNAs revealed several key lncRNAs such as MSTRG.604204 and MSTRG.604206 might associated with lipid metabolic. Tissue specific analysis indicated that circRNA exhibited the highest tissue specificity than lncRNA and mRNA, and the IAT had the most tissue specific lncRNA, mRNA, and circRNA compared with other tissues. Taken together, this study gives us a novel clue to the role of mRNAs, lncRNAs and circRNAs in fat metabolism, thus improving our understanding of the regulation mechanism of different gene expression profiles in adipose deposition
2019-02-09 | GSE110478 | GEO